On 5/30/12 7:42 AM, Stephen Cox wrote:
Hi Justin,
Thanks for getting back and posting the links.
On 5/29/12 6:22 AM, Stephen Cox wrote:
> Hi,
>
> I'm running a number of energy minimizations on a clathrate supercell and
I get
> quite significantly different values for the total energy depending on
the
> number of mpi processes / number of threads I use. More specifically,
some
> numbers I get are:
>
> #cores energy
> 1 -2.41936409202696e+04
> 2 -2.43726425776809e+04
> 3 -2.45516442350804e+04
> 4 -2.47003944216983e+04
>
> #threads energy
> 1 -2.41936409202696e+04
> 2 -2.43726425776792e+04
> 3 -2.45516442350804e+04
> 4 -2.47306458924815e+04
>
>
> I'd expect some numerical noise, but these differences seem to0 large for
that.
The difference is only 2%, which by MD standards, is quite good, I'd say ;)
Consider the discussion here:
I agree for MD this wouldn't be too bad, but I'd expect energy minimization to
get very close to the same local minimum from a given starting configuration.
The thing is I want to compute a binding curve for my clathrate and compare to
DFT values for the binding energy (amongst other things), and the difference in
energy between different number of cores is rather significant for this purpose.
I think the real issue comes down to how you're going to calculate binding
energy. I would still expect that with sufficient MD sampling, the differences
should be small or statistically insignificant given the nature of MD
calculations. EM will likely be very sensitive to the nature of how it is run
(MPI vs. serial, etc) since even the tiny rounding errors and other factors
described below will cause changes in how the EM algorithm proceeds. For most
purposes, such differences are irrelevant as EM is only a preparatory step for
more intense calculations.
Furthermore, if I only calculate the energy for nsteps = 0 (i.e. a single point
energy for identical structures) I get the same trend as above (both mpi/openmp
with domain/particle decomposition). Surely there shouldn't be such a large
difference in energy for a single point calculation?
That depends. Are you using the same .mdp file, just setting "nsteps = 0"? If
so, that's not a good test. EM algorithms will make a change at step 0, the
magnitude of which will again reflect the differences you're seeing. If you use
the md integrator with a zero-step evaluation, that's a better test.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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